[gmx-users] Regarding Umbrella samplling
jalemkul at vt.edu
Tue Sep 30 02:43:16 CEST 2014
On 9/29/14 10:09 AM, Sathish Kumar wrote:
> Dear gromacs usres,
> I have run the umbrella sampling with the help of tutorial of justin....In
> my system rna is binding with gold nanoparticle...to find out the binding
> energy i run the umbrella sampling using the space 0.2 nm and i got total
> 59 configurations, each configuration was run for 5 ns. The profile files
> are shared with the link below.
> In the profile image, i have not got the plateu value, can i take the
> difference between final and starting pmf values for the binding enrgy.
> Please give suggestions.
You don't have either a plateau or a defined minimum, so I'd say that the
reaction coordinate is incomplete, either in terms of the sampling within the
windows or the window setup itself.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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